Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate Pf6N2E2_4195 transport permease protein of gamma-aminobutyrate
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4195 Length = 464 Score = 308 bits (789), Expect = 3e-88 Identities = 160/424 (37%), Positives = 246/424 (58%), Gaps = 3/424 (0%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L +GLK RH+ M++I G IG GLF+G+G AIA AGP ++L+YA G + +MR LGE+ Sbjct: 10 LEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRMLGEMA 69 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 + P +GSF+TYA+ +G +AGF GW YW+ WV+ E A A +H WFP+V W Sbjct: 70 VASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVAIWAF 129 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 L +L + N +V +GE EFWFAL+KVV I+ I +G+ I FGV P + S+ Sbjct: 130 TLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGVMAI-FGVLPTSQVSGVSH 188 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 L+ GF+P G V+ + MF++ G E++ + A E++NP + + ATN V+WRI +F Sbjct: 189 LFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGLF 248 Query: 259 YVGALIIMMALVPWNE-LKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFST 317 Y+ ++ I++ALVPWN+ L V + V ER+G+P A IV++VV+ A S NS +++ Sbjct: 249 YLVSIFIVVALVPWNDPLLASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCLNSALYTA 308 Query: 318 GRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISL 377 RM+++L + G AP R + P A+ S + V NY+ P VF ++ + S Sbjct: 309 SRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTGAAFLAVFANYVAPAAVFDFLLASSG 368 Query: 378 VGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGT 437 +L + +I ++ L RK A R + VAF M P + V+ F++ ++ Sbjct: 369 AIALLVYLVIAVSQLRMRKQRMA-RGEKVAFSMWLFPGLTYAVIVFIVGALTIMLFQEAH 427 Query: 438 RVAL 441 RV + Sbjct: 428 RVEI 431 Lambda K H 0.328 0.142 0.445 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 716 Number of extensions: 47 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 472 Length of database: 464 Length adjustment: 33 Effective length of query: 439 Effective length of database: 431 Effective search space: 189209 Effective search space used: 189209 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory